Theoretical neuroscience:
Single neuron dynamics and computation
STAT 42510 - CPNS 35510
Instructor:
Nicolas Brunel
nbrunel@uchicago.edu
TA:
Ang Li
anglipku@gmail.com
Practical details
First course in a 3-course series:
• Single neuron dynamics and computation (Fall, STAT 42510 - CPNS 35510)
Instructor: Nicolas Brunel
• Network dynamics and computation (Winter, STAT 42520 - CPNS 35520)
Instructor: Nicolas Brunel
• Statistics and information theory (Spring, STAT 42600 - CPNS 35600)
Instructor: Stephanie Palmer
Practical details
• Problem sets will be issued every Tuesday from Week 2 to Week 9 (total of 7), and due
the next Tuesday in class.
• A take-home final will be issued on December 4, and due on December 18 in my office
(Eckhart 106)
• Grades: Problem sets will account for 50% of the grade; The take-home final for the
remaining 50%.
• TA: Ang Li (anglipku@gmail.com)
• Office hours: Thursday 5pm, E29 (Ang Li); Friday 4pm, E106 (Nicolas Brunel)
Introduction
• Brains, scales, structure, dynamics
• What is computational/theoretical neuroscience?
• Brief history of computational/theoretical neuroscience
• Outline of the course
The human brain: a network of 1011 neurons connected by 1015
synapses
Networks: from C Elegans to Humans
C Elegans
302
5,000
Fruit fly
105
107
Honey bee
106
109
Mouse
108
1011
Cat
109
1012−13
1011
1015
Human
Spatial scales of the brain
∼10cm
Whole brain
∼1cm
Brain structure/cortical areas
100µm- 1mm
Local network/‘column’/‘module’
10µm- 1mm
Neuron
100nm- 1µm
Sub-cellular compartments
∼10nm
Channel, receptor, intracellular protein
Experimental tools
Brain level
• Brains are interconnected networks of
structures/areas
Area level
• Areas are interconnected networks of local networks (‘columns’)
Local network level
• Size ∼ cubic mm
• Total number of cells ∼ 100,000
• Total number of synapses ∼ 109
(10,000 per neuron)
– pyramidal cells - excitatory (80%)
• Cells connect potentially to all other cell
types (E→ E, E→ I, I→ E, I→ I)
– interneurons - inhibitory (20%)
• Connection probability ∼ 10%
• Types of cells:
Neuron level
• Neuron = complex tree-like structures with many compartments (e.g. dendritic spines)
Subcellular compartment level
• Subcellular compartments (e.g. dendritic spines) contain a huge diversity of molecules
(in particular protein kinases and phosphatases) whose interactions define complex
networks
The many temporal scales of the brain
Days-Years
Long-term memory
Seconds-Minutes
Short-term (working) memory
100ms - 1s
Behavioral time scales/Reaction times
∼ 10ms
Single neuron/synaptic time scales
∼ 1ms
Action potential duration; local propagation delays
1ms
Channel opening/closing
Experimental tools for observing the brain
Submillisecond
• Molecular time scales (channel opening/closing; diffusion of neurotransmitter in
synaptic cleft; etc)
Millisecond
• Width of action potentials; axonal delays in local networks
Tens of ms
• Synaptic decay time constants; membrane time constant of neurons; axonal delays for
long-range connections
Hundreds of ms
• Behavioral time scales (e.g. motor response to a stimulus)
Seconds-minutes
• Short-term memory
Working memory
Days-years
• Long-term memory
What is theoretical neuroscience?
(a.k.a. computational neuroscience;
includes neuromathematics; neurophysics; neurostatistics; neuroinformatics)
Using quantitative tools (from mathematics/statistics/computer science/physics) to advance
our understanding of how brains work.
Questions in theoretical neuroscience
What? Describe in a mathematically compact form a set of experimental observations.
How? Understand how a neural system
produces a given behavior.
Why? Understand why a neural system
performs the way it does, using e.g.
tools from information theory.
Methods - numerical
• Numerical simulations
– Write your own code (e.g.in C, C++)
– Use available software
∗
∗
∗
∗
Dedicated software for single neuron models: Neuron, Genesis
Dedicated software for network simulations: NEST
Matlab
Brian
Methods - analytical
• Analytical methods
– Single neuron/synapse models: systems of coupled differential equations. Tools of
dynamical systems (linear stability analysis, bifurcation theory)
– Networks: Graph theory, linear algebra. Large N limit: tools of statistical physics
– Noise: ubiquitous at all levels of the nervous system. Statistics, probability theory,
stochastic processes.
– Coding: Information theory
A few historical landmarks
Before mid-1980s: a few isolated pioneers
• 1907: Louis Lapicque (leaky integrate-and-fire neuron)
• 1940s: Warren McCulloch, Walter Pitts (binary neurons, neural networks)
• 1940s: Donald Hebb (neuronal assemblies, synaptic plasticity)
• 1940s-50s: Alan Hodgkin, Andrew Huxley (model for AP generation)
• 1950s: Wilfrid Rall (cable theory)
• 1950s: Frank Rosenblatt (perceptron)
• 1960s: Horace Barlow (coding in sensory systems)
• 1960s-70s: David Marr (systems-level models of cerebellum/neocortex/hippocampus)
• 1970s: Hugh Wilson, Jack Cowan, Shun-Ishi Amari (‘rate models’)
• 1980s: John Hopfield, Daniel Amit, Hanoch Gutfreund, Haim Sompolinsky (associative
memory models)
A few historical landmarks
From the 1990s: establishment of a field
• First annual computational neuroscience conference in 1992 (now two main
conferences/year, CNS and Cosyne, each around 500 participants per year)
• Many specialized journals created from the beginning of the 1990s (Neural
Computation; Network; Journal of Computational Neuroscience; Frontiers in
Computational Neuroscience; etc)
• Annual computational neuroscience summerschools since mid-1990s (Woodshole,
ACCN in Europe, Okinawa, CSHL China)
• Birth of major Computational Neuroscience centers in the US (1990s, Sloan-Swartz),
Israel (HU, 1990s) and Europe (Gatsby Unit, Bernstein Centers, 2000s)
• Now widely accepted as an integral part of neuroscience (theory papers routinely
published in major neuroscience journals)
Week 1
Week 2
Week 3
Sept 30
Oct 2
Biophysics, Hodgkin-Huxley (HH) model
Oct 7
2D models for spike generation
Oct 9
Ionic channels and firing behaviors
Oct 14
From HH to leaky integrate-and-fire (LIF) neurons
Oct 16
Stochastic dynamics of neurons
Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Introduction
No classs
Oct 28
From LIF to ‘firing rate’ and binary neurons
Oct 30
Axons
Nov 4
Dendrites
Nov 6
Synapses
Nov 11
Plasticity
Nov 13
Coding I
Nov 18
Coding II
Nov 20
Decoding
Nov 25
Unsupervised learning
Nov 27
No class
Dec 2
Supervised learning
Dec 4
Reinforcement learning
Spatial scales of the brain
∼10cm
Whole brain
∼1cm
Cortical area; other brain structure
100µm- 1mm
Local network/‘column’/‘module’
10µm- 1mm
Neuron
100nm- 1µm
Sub-cellular compartments
∼1-10nm
Molecules (channels, receptors, etc)
Single neuron models
• Hodgkin-Huxley neuron
X
dV
C
dt
= −IL (V )−
Ia (V, ma , ha )+Isyn (t)
a
IL (V )
=
gL (V − VL )
Ia (V, ma , ha )
dma
τma (V )
dt
dha
τha (V )
dt
=
a ya
ga (V − Va )mx
a ha
=
−ma + m∞
a (V )
=
−ha + h∞
a (V )
• Integrate-and-fire neuron
C
dV
= −gL (V − VL ) + Isyn (t)
dt
Fixed threshold Vt , reset Vr , refractory period;
• How do single neurons work?
• What are the mechanisms of action potential generation?
• How do neurons transform synaptic inputs into a train of action potentials?
Single synapses
• ‘Conductance-based’
X
Ii,syn (t)
=
(V − Va )
=
ga,i,j sa (t − tkj )
j,k
a=E,I
τa ṡa
X
...
• ‘Current-based’
Ii,syn (t)
=
X X
Ja,i,j sa (t − tkj )
a=E,I j,k
Popular choices of s
– Delayed difference of exponential;
– Delayed delta function
• How do synapses work?
• What are the mechanisms for synaptic
plasticity on short time scales?
Synaptic plasticity
Synaptic efficacy can be modified in various ways:
• Spike timing
(STDP experiments)
• Firing rate
(BCM, Sjostrom et al, etc)
• Post-synaptic V
(pairing, etc)
• Can we capture this experimental data using simplified ‘plasticity rules’?
• What are the mechanisms of induction of synaptic plasticity?
Learning in a single neuron: the perceptron
• N synapses/inputs;
input patterns
synaptic
weights
A
B
w1
0
1
w2
1
0
w3
0
1
w4
1
0
parallel
fibres
1
2
3
4
• sums linearly its inputs;
• emits a spike if inputs > θ ∼ 10
mV (threshold)
• has to learn a set of p ≡ αN input/output associations
Purkinje
cell
threshold
(θ ± κ)
B
0
A
1
output
• by appropriate choice of its synaptic weights wi ≥ 0.
• in a robust way (as measured by κ);
• can be achieved using simple
learning algorithms
• How much information can a single neuron/a population of neurons store?
• What kind of learning algorithms/rules allow to reach optimal storage?
Useful books
• Tuckwell, “Introduction to Theoretical Neurobiology”, Vols. I & II (Cambridge U. Press, 1988)
• Amit, “Modeling brain function: The world of attractor neural networks” (Cambridge U. Press, 1989)
• Hertz, Krogh, and Palmer, “Introduction to the Theory of Neural Computation” (Addison-Wesley, 1991 - now
from: Perseus Book Group and Westview Press)
• Rieke, Warland, de Ruyter van Steveninck, and Bialek, “Spikes: Exploring the Neural Code” (MIT Press,
1997)
• Koch, “Biophysics of Computation: Information Processing in Single Neurons” (Oxford U. Press, 1999)
• Dayan and Abbott, “Theoretical Neuroscience: Computational and Mathematical Modeling of Neural
Systems” (MIT Press, 2001)
• Izhikevich, “Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting” (MIT Press,
2007)
• Ermentrout and Terman, “Mathematical Foundations of Neuroscience” (Springer, 2010)
• Gerstner, Kistler, Naud and Paninski “Neuronal Dynamics: From single neurons to networks and models of
cognition” (Cambridge U. Press, 2014)